Xgraft - GSEA and ORA Figures
library(xlsx)
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## ========================================1 KHOS Xgraft
PATH = "/lustre06/project/6004736/alvann/from_narval/220318_EZHIP/RNA/xgrafts/out/01_raptor_exprtools/KHOS/"
PATH_GSEA_ORA = "/lustre06/project/6004736/alvann/from_narval/220318_EZHIP/RNA/xgrafts/out/02_GSEA_ORA/KHOS/"
COMP = "WTvsEZHIP"
CELL = 'KHOS'deg.khos = read.csv(paste(PATH, "diff/hg19.Ensembl.ensGene.exon/", COMP, '.tsv', sep=""), sep="\t")
counts.khos = read.csv(paste(PATH, "counts/hg19.Ensembl.ensGene.exon.norm.tsv.gz", sep=""), sep="\t")load(paste0(PATH_GSEA_ORA, CELL, '_', COMP, '.Rda'))write.xlsx(GOBP %>% as.data.frame(), file=paste0(PATH_GSEA_ORA, "KHOS_xgraft_GSEA.xlsx"), sheetName="GOBP", row.names=FALSE)
write.xlsx(Hall %>% as.data.frame(), file=paste0(PATH_GSEA_ORA, "KHOS_xgraft_GSEA.xlsx"), sheetName="HALLMARK", append=TRUE, row.names=FALSE)Hall %>% as.data.frame()p = (Hall_ora_up %>% as.data.frame())[1:10,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +Count), y = Count, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
scale_y_continuous(expand = c(0,0)) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Hallmark')) +
coord_flip()## Warning: There was 1 warning in `mutate()`.
## ℹ In argument: `across("ID", str_replace_all, "_", " ")`.
## Caused by warning:
## ! The `...` argument of `across()` is deprecated as of dplyr 1.1.0.
## Supply arguments directly to `.fns` through an anonymous function instead.
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## # Previously
## across(a:b, mean, na.rm = TRUE)
##
## # Now
## across(a:b, \(x) mean(x, na.rm = TRUE))## Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
## ℹ Please use the `linewidth` argument instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_ORA_UP_Hallmark_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (Hall %>% as.data.frame())[1:20,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Hallmark')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_UP_Hallmark_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p2 = gseaplot2(Hall,
geneSetID = c('KRAS_SIGNALING_UP', 'MYOGENESIS', 'EPITHELIAL_MESENCHYMAL_TRANSITION'),
color = c('#337357', '#CD5334', '#FFB41F'))
p2
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_HALLMARK_GSEA_plot.pdf"), width = 7, height = 5)
p2
dev.off()## png
## 2p = (GOBP_ora_up %>% as.data.frame())[1:10,] %>%
mutate(sign = ifelse(p.adjust < 0.01, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +Count), y = Count, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
scale_y_continuous(expand = c(0,0)) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - GOBP')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_ORA_UP_GOBP_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (dolgalev_atlas %>% as.data.frame())[1:14,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' Xeno - Dolgalev')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Dolgalev_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (baryawno_atlas %>% as.data.frame())[1:15,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' Xeno - Baryawno')) +
coord_flip() +
scale_y_continuous(expand = c(0,0))
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Baryawno_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (baccin_atlas %>% as.data.frame())[1:15,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' Xeno - Baccin')) +
coord_flip() +
scale_y_continuous(expand = c(0,0))
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Baccin_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (zhang_atlas %>% as.data.frame())[1:10,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' Xeno - Zhang')) +
coord_flip() +
scale_y_continuous(expand = c(0,0))
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Zhang_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 22 MG63 Xgraft
PATH = "/lustre06/project/6004736/alvann/from_narval/220318_EZHIP/RNA/xgrafts/out/01_raptor_exprtools/MG63/"
PATH_GSEA_ORA = "/lustre06/project/6004736/alvann/from_narval/220318_EZHIP/RNA/xgrafts/out/02_GSEA_ORA/MG63/"
COMP = "WTvsEZHIP"
CELL = 'MG63'deg.mg63 = read.csv(paste(PATH, "diff/hg19.Ensembl.ensGene.exon/", COMP, '.tsv', sep=""), sep="\t")
counts.mg63 = read.csv(paste(PATH, "counts/hg19.Ensembl.ensGene.exon.norm.tsv.gz", sep=""), sep="\t")load(paste0(PATH_GSEA_ORA, CELL, '_', COMP, '.Rda'))p = (dolgalev_atlas %>% as.data.frame())[1:14,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' Xeno - Dolgalev')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Dolgalev_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (baryawno_atlas %>% as.data.frame())[1:15,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' Xeno - Baryawno')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Baryawno_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (baccin_atlas %>% as.data.frame())[1:15,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' Xeno - Baccin')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Baccin_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (zhang_atlas %>% as.data.frame())[1:10,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' Xeno - Zhang')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Zhang_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2write.xlsx(GOBP %>% as.data.frame(), file=paste0(PATH_GSEA_ORA, "MG63_xgraft_GSEA.xlsx"), sheetName="GOBP", row.names=FALSE)
write.xlsx(Hall %>% as.data.frame(), file=paste0(PATH_GSEA_ORA, "MG63_xgraft_GSEA.xlsx"), sheetName="HALLMARK", append=TRUE, row.names=FALSE)Hall_ora_up %>% as.data.frame()CA2/PRRX1/SATB1/PTGS2/CPE/EPB41L3/GPRC5B/SERPINA3/MMP9/BMP2/RGS16/RELN/NAP1L2/ID2/SPP1/CCND2/MMP11/ACE/IL1B/TNFRSF1B
p = (Hall_ora_up %>% as.data.frame())[1:10,] %>%
mutate(sign = ifelse(p.adjust < 0.1, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +Count), y = Count, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('#E26565'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.1', '>0.1')) +
scale_y_continuous(expand = c(0,0)) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Hallmark')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_ORA_UP_Hallmark_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (Hall %>% as.data.frame())[1:20,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Hallmark')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_UP_Hallmark_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2genes = str_split((Hall_ora_up %>% as.data.frame() %>% filter(ID == "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION"))$geneID, pattern = '/')
h = counts.mg63 %>%
rownames_to_column('ID') %>%
separate(ID, into = c('ENS', 'SYM'), sep = ":") %>%
filter(SYM %in% genes[[1]]) %>%
select(-ENS) %>%
column_to_rownames('SYM')
h = scale(t(h)) %>%
t()
col_fun = colorRamp2(c(-2, 0, 2), c("steelblue", "beige", "firebrick"))
h1 = Heatmap(h,
col = col_fun,
name = 'z-score',
width = ncol(h)*unit(5, "mm"),
height = nrow(h)*unit(4, "mm"),
show_column_names = F,
show_row_dend = F,
column_title = 'EMT',
bottom_annotation = HeatmapAnnotation(Cond = c(rep('EZHIP', 3), rep('WT', 2)),
col = list(Cond = c('EZHIP' = "red", 'WT' = "blue"))))
draw(h1)
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION.pdf"), width = 10, height = 10)
draw(h1)
dev.off()## png
## 2Hall %>% as.data.frame()p2 = gseaplot2(Hall,
geneSetID = c('KRAS_SIGNALING_UP', 'MYOGENESIS', 'EPITHELIAL_MESENCHYMAL_TRANSITION'),
color = c('#337357', '#CD5334', '#FFB41F'))
p2
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_HALLMARK_GSEA_plot.pdf"), width = 7, height = 5)
p2
dev.off()## png
## 2p = (GOBP_ora_up %>% as.data.frame())[1:10,] %>%
mutate(sign = ifelse(p.adjust < 0.005, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +Count), y = Count, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
scale_y_continuous(expand = c(0,0)) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Hallmark')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_ORA_UP_GOBP_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 23 U2OS Cell Line
PATH = "/lustre06/project/6004736/alvann/from_narval/220318_EZHIP/RNA/U2OS/out/01_raptor_exprtools/EZHIP_minus_C77_C2/"
PATH_GSEA_ORA = "/lustre06/project/6004736/alvann/from_narval/220318_EZHIP/RNA/U2OS/out/02_GSEA_ORA_minus_C77_C2//"
COMP = "EZHIP_KOvsEZHIP"
CELL = 'U2OS'deg.u2os = read.csv(paste(PATH, "diff/Ensembl.ensGene.exon/", COMP, '.tsv', sep=""), sep="\t")
counts.u2os= read.csv(paste(PATH, "counts/Ensembl.ensGene.exon.raw.tsv.gz", sep=""), sep="\t")load(paste0(PATH_GSEA_ORA, CELL, '_', COMP, '.Rda'))p = (dolgalev_atlas %>% as.data.frame())[1:14,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Dolgalev')) +
coord_flip() +
scale_y_continuous(expand = c(0, 0))
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Dolgalev_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (baryawno_atlas %>% as.data.frame())[1:15,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Baryawno')) +
coord_flip() +
scale_y_continuous(expand = c(0, 0))
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Baryawno_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (baccin_atlas %>% as.data.frame())[1:15,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Baccin')) +
coord_flip() +
scale_y_continuous(expand = c(0, 0))
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Baccin_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (zhang_atlas %>% as.data.frame())[1:10,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Zhang')) +
coord_flip() +
scale_y_continuous(expand = c(0, 0))
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Zhang_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2write.xlsx(GOBP %>% as.data.frame(), file=paste0(PATH_GSEA_ORA, "U2OS_cell_line_GSEA.xlsx"), sheetName="GOBP", row.names=FALSE)
write.xlsx(Hall %>% as.data.frame(), file=paste0(PATH_GSEA_ORA, "U2OS_cell_line_GSEA.xlsx"), sheetName="HALLMARK", append=TRUE, row.names=FALSE)Hall %>% as.data.frame()p = (Hall_ora_up %>% as.data.frame())[1:10,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +Count), y = Count, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
scale_y_continuous(expand = c(0,0)) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Hallmark')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_ORA_UP_Hallmark_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (Hall %>% as.data.frame())[1:20,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Hallmark')) +
coord_flip() +
scale_y_continuous(expand = c(0,0))
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Hallmark_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2genes = str_split((Hall_ora_up %>% as.data.frame() %>% filter(ID == "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION"))$geneID, pattern = '/')
h = cbind(counts.khos, counts.mg63) %>%
rownames_to_column('ID') %>%
separate(ID, into = c('ENS', 'SYM'), sep = ":") %>%
filter(SYM %in% genes[[1]]) %>%
select(-ENS) %>%
column_to_rownames('SYM')
h = scale(t(h)) %>%
t()
col_fun = colorRamp2(c(-2, 0, 2), c("steelblue", "beige", "firebrick"))
h1 = Heatmap(h,
col = col_fun,
name = 'z-score',
width = ncol(h)*unit(5, "mm"),
height = nrow(h)*unit(4, "mm"),
show_column_names = F,
show_row_dend = F,
column_title = 'EMT',
bottom_annotation = HeatmapAnnotation(Cond = c(rep('EZHIP', 3), rep('WT', 3), rep('EZHIP', 3), rep('WT', 2)),
`Cell line` = c(rep('KHOS', 6), rep('MG63', 5)),
col = list(Cond = c('EZHIP' = "red", 'WT' = "blue"))))
draw(h1)
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION.pdf"), width = 10, height = 10)
draw(h1)
dev.off()## png
## 2p2 = gseaplot2(Hall,
geneSetID = c('KRAS_SIGNALING_UP', 'MYOGENESIS', 'EPITHELIAL_MESENCHYMAL_TRANSITION'),
color = c('#337357', '#CD5334', '#FFB41F'))
p2
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_HALLMARK_GSEA_plot.pdf"), width = 7, height = 5)
p2
dev.off()## png
## 2p = (GOBP_ora_up %>% as.data.frame())[1:10,] %>%
mutate(sign = ifelse(p.adjust < 0.005, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +Count), y = Count, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
scale_y_continuous(expand = c(0,0)) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - GOBP')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_ORA_UP_GOBP_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 24 hMSC Cell Line
PATH = "/lustre06/project/6004736/alvann/from_narval/220318_EZHIP/RNA/hMSC/out/01_raptor_exprtools/EZHIP/"
PATH_GSEA_ORA = "/lustre06/project/6004736/alvann/from_narval/220318_EZHIP/RNA/hMSC/out/02_GSEA_ORA/"
COMP = "WTvsEZHIP"
CELL = 'hMSC'deg.hMSC.cell = read.csv(paste(PATH, "diff/Ensembl.ensGene.exon/", COMP, '.tsv', sep=""), sep="\t")
counts.hMSC.cell = read.csv(paste(PATH, "counts/Ensembl.ensGene.exon.raw.tsv.gz", sep=""), sep="\t")load(paste0(PATH_GSEA_ORA, CELL, '_', COMP, '.Rda'))p = (dolgalev_atlas %>% as.data.frame())[1:14,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Dolgalev')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Dolgalev_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (baryawno_atlas %>% as.data.frame())[1:15,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Baryawno')) +
coord_flip() +
scale_y_continuous(expand = c(0, 0))
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Baryawno_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (baccin_atlas %>% as.data.frame())[1:15,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Baccin')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Baccin_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (zhang_atlas %>% as.data.frame())[1:10,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Zhang')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Zhang_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2write.xlsx(GOBP %>% as.data.frame(), file=paste0(PATH_GSEA_ORA, CELL, "_xgraft_GSEA.xlsx"), sheetName="GOBP", row.names=FALSE)
write.xlsx(Hall %>% as.data.frame(), file=paste0(PATH_GSEA_ORA, CELL, "_xgraft_GSEA.xlsx"), sheetName="HALLMARK", append=TRUE, row.names=FALSE)Hall %>% as.data.frame()p = (Hall_ora_up %>% as.data.frame())[1:10,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +Count), y = Count, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
scale_y_continuous(expand = c(0,0)) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Hallmark')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_ORA_UP_Hallmark_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (Hall %>% as.data.frame())[1:20,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Hallmark')) +
coord_flip()
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Hallmark_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2GOBP %>% as.data.frame()p = (GOBP_ora_up %>% as.data.frame())[1:10,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +Count), y = Count, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
scale_y_continuous(expand = c(0,0)) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Hallmark')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_ORA_UP_Hallmark_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (GOBP %>% as.data.frame())[1:20,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Hallmark')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_GOBP_barplot.pdf"), width = 10, height = 5)
p
dev.off()## png
## 25 MG63 Cell Line
PATH = "/lustre06/project/6004736/alvann/from_narval/220318_EZHIP/RNA/MG63/out/01_raptor_exprtools/EZHIP/"
PATH_GSEA_ORA = "/lustre06/project/6004736/alvann/from_narval/220318_EZHIP/RNA/MG63/out/02_GSEA_ORA/"
COMP = "WTvsEZHIP"
CELL = 'MG63'deg.mg63.cell = read.csv(paste(PATH, "diff/Ensembl.ensGene.exon/", COMP, '.tsv', sep=""), sep="\t")
counts.mg63.cell = read.csv(paste(PATH, "counts/Ensembl.ensGene.exon.raw.tsv.gz", sep=""), sep="\t")load(paste0(PATH_GSEA_ORA, CELL, '_', COMP, '.Rda'))p = (dolgalev_atlas %>% as.data.frame())[1:14,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Dolgalev')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Dolgalev_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (baryawno_atlas %>% as.data.frame())[1:15,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Baryawno')) +
coord_flip() +
scale_y_continuous(expand = c(0, 0))
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Baryawno_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (baccin_atlas %>% as.data.frame())[1:15,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Baccin')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Baccin_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (zhang_atlas %>% as.data.frame())[1:10,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Zhang')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Zhang_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2write.xlsx(GOBP %>% as.data.frame(), file=paste0(PATH_GSEA_ORA, CELL, "_xgraft_GSEA.xlsx"), sheetName="GOBP", row.names=FALSE)
write.xlsx(Hall %>% as.data.frame(), file=paste0(PATH_GSEA_ORA, CELL, "_xgraft_GSEA.xlsx"), sheetName="HALLMARK", append=TRUE, row.names=FALSE)write.xlsx(GOBP %>% as.data.frame(), file=paste0(PATH_GSEA_ORA, CELL, "_xgraft_GSEA.xlsx"), sheetName="GOBP", row.names=FALSE)
write.xlsx(Hall %>% as.data.frame(), file=paste0(PATH_GSEA_ORA, CELL, "_xgraft_GSEA.xlsx"), sheetName="HALLMARK", append=TRUE, row.names=FALSE)Hall %>% as.data.frame()p = (Hall_ora_up %>% as.data.frame())[1:10,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +Count), y = Count, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
scale_y_continuous(expand = c(0,0)) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Hallmark')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_ORA_UP_Hallmark_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (Hall %>% as.data.frame())[1:20,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Hallmark')) +
coord_flip()
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Hallmark_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 26 KHOS Cell Line
PATH = "/lustre06/project/6004736/alvann/from_narval/220318_EZHIP/RNA/KHOS/out/01_raptor_exprtools/EZHIP/"
PATH_GSEA_ORA = "/lustre06/project/6004736/alvann/from_narval/220318_EZHIP/RNA/KHOS/out/02_GSEA_ORA/"
COMP = "WTvsEZHIP"
CELL = 'KHOS'deg.khos.cell = read.csv(paste(PATH, "diff/Ensembl.ensGene.exon/", COMP, '.tsv', sep=""), sep="\t")
counts.khos.cell = read.csv(paste(PATH, "counts/Ensembl.ensGene.exon.raw.tsv.gz", sep=""), sep="\t")load(paste0(PATH_GSEA_ORA, CELL, '_', COMP, '.Rda'))p = (dolgalev_atlas %>% as.data.frame())[1:14,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Dolgalev')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Dolgalev_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (baryawno_atlas %>% as.data.frame())[1:15,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Baryawno')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Baryawno_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (baccin_atlas %>% as.data.frame())[1:15,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Baccin')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Baccin_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (zhang_atlas %>% as.data.frame())[1:10,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Zhang')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Zhang_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2write.xlsx(GOBP %>% as.data.frame(), file=paste0(PATH_GSEA_ORA, CELL, "_xgraft_GSEA.xlsx"), sheetName="GOBP", row.names=FALSE)
write.xlsx(Hall %>% as.data.frame(), file=paste0(PATH_GSEA_ORA, CELL, "_xgraft_GSEA.xlsx"), sheetName="HALLMARK", append=TRUE, row.names=FALSE)Hall %>% as.data.frame()p = (Hall_ora_up %>% as.data.frame())[1:10,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +Count), y = Count, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
scale_y_continuous(expand = c(0,0)) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Hallmark')) +
coord_flip()
p
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_ORA_UP_Hallmark_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2p = (Hall %>% as.data.frame())[1:20,] %>%
mutate(sign = ifelse(p.adjust < 0.05, 'p.adjust < 0.05', NA)) %>%
mutate(across('ID', str_replace_all, '_', ' '),
across('ID', str_replace_all, 'HALLMARK', ' ')) %>%
ggplot(aes(x = reorder(ID, +NES), y = NES, fill = sign)) +
geom_bar(stat = 'identity') +
scale_fill_manual(values = c('firebrick'), na.value = 'lightgrey', name = 'p-val', labels = c('<0.05', '>0.05')) +
theme_bw() +
theme(text = element_text(size = 15),
axis.title.y = element_blank(),
axis.line = element_line(size = 0.5),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
ggtitle(paste0(CELL, ' - Hallmark')) +
coord_flip()
pdf(paste0(PATH_GSEA_ORA, CELL, '_', COMP, "_GSEA_Hallmark_barplot.pdf"), width = 7, height = 5)
p
dev.off()## png
## 2